Mercurial > repos > peterjc > mira_datatypes
diff mira.py @ 85:59500bcfaf82 draft default tip
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/datatypes/mira_datatypes commit f7e6686f564972fb2892bec8da890565bb41e0ac-dirty
author | peterjc |
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date | Mon, 01 Jul 2019 14:02:09 -0400 |
parents | 8d7684a3346a |
children |
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--- a/mira.py Mon Jul 01 13:28:59 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -"""MiraAssemblyFormat class for the 'mira' format within Galaxy.""" - -from galaxy.datatypes.data import Text - - -class MiraAssemblyFormat(Text): - """MIRA Assembly Format data.""" - - file_ext = "mira" - - def sniff(self, filename): - """Determine if the file is a MIRA Assembly Format file. - - Note currently this only detects MIRA Assembly Format v2.0, - as used in MIRA v3.9 and v4.0. - - It does not detect MIRA Assembly Format v1 as used in both - MIRA v3.2 and v3.4. - """ - h = open(filename) - line = h.readline() - if line.rstrip() != "@Version\t2\t0": - h.close() - return False - line = h.readline() - if line.rstrip() != "@Program\tMIRALIB": - h.close() - return False - return True - - def merge(split_files, output_file): - """Merge MIRA assembly files (not implemented). - - Merging multiple MIRA files is non-trivial and may not be possible... - """ - if len(split_files) == 1: - # For one file only, use base class method (move/copy) - return Text.merge(split_files, output_file) - if not split_files: - raise ValueError( - "No MIRA files to merge, %r, into %r" % (split_files, output_file) - ) - raise NotImplementedError( - "Merging MIRA Assembly Files has not been implemented" - ) - - merge = staticmethod(merge) - - def split(cls, input_datasets, subdir_generator_function, split_params): - """Split a MIRA Assembly File (not implemented for now).""" - if split_params is None: - return None - raise NotImplementedError("Can't yet split a MIRA Assembly Format file") - - merge = staticmethod(merge)